The present invention provides a semiconductor device and a manufacturing method thereof, and relates to the semiconductor technology field. The method comprises: providing a semiconductor substrate,and forming a grid structure on the surface of the semiconductor substrate, wherein gap wall structures are formed at two sides of the grid structure; forming a groove in a PMOS area of the semiconductor substrate, wherein the groove is used for epitaxial growth of an embedded silicon-germanium layer; performing high-temperature baking processing under an H2 atmosphere; performing cleaning processing through adoption of the wet method; and performing epitaxial growth of the embedded silicon-germanium layer in the groove. According to the invention, the semiconductor device and the manufacturing method thereof can effectively remove pollution, reduce the problems of impurity generation and growth dislocation when epitaxial growth of an embedded silicon-germanium layer is performed and improve performances and a yield of an FinFET device.